Why 3‐D? Gel‐based microarrays in proteomics

Abstract

Gel-based microarrays (biochips) consisting of nanoliter and sub-nanoliter gel drops on hydrophobic substrate are a versatile technology platform for immobilization of proteins and other biopolymers. Biochips provide a highly hydrophilic environment, which stabilizes immobilized molecules and facilitates their interactions with analytes. The probes are immobilized simultaneously with gel polymerization, evenly distributed throughout individual elements, and are easily accessible because of large pores. Each element is an isolated nanotube. Applications of biochips in the studies of protein interactions with other proteins, nucleic acids, and glycans are described. In particular, biochips are compatible with MALDI-MS. Biochip-based assay of prostate-specific antigen became the first protein microarray approved for clinical use by a national regulatory agency. In this review, 3-D immobilization is compared with mainstream technologies based on surface immobilization.

Protein immobilization techniques for microfluidic assays

“…Thus, involved chemical surface preparation is generally required to induce surface functional groups for protein immobilization. 9,35,[77][78][79][80] As immobilization on planar surfaces yields limited protein density, three dimensional (3-D) structures have been employed inside microfluidic channels for higher protein capture capacity, 21,22,81 resulting in improved immunoassay sensitivity or enzyme conversion rates (Figure 1(b)). 3-D structures have been created by patterning microstructures (e.g., microposts 29,82,83 and micropits 60 ) or through insertion of porous membranes 67,84,85 before assembly of microfluidic chips.…”

“…The increased effective surface area found in the 3-D material offers a larger number of immobilization sites, as compared to channel wall (2-D) systems. 21,22,81 Back-of-the-envelope estimates suggest that three-dimensional gel structures provide about 100 $ 1000 fold increase in binding sites, as compared to immobilization sites on capillary or microchannel walls alone. 21 Importantly, the diffusion length between reaction partners (e.g., antibody and antigen, or enzyme and substrate) is reduced when the immobilized partner is in a 3-D material, as opposed to patterned on a microchannel or even nanochannel wall.…”

Diagnostics of Molecular Markers in Childhood Acute Leukaemia Using Biochips

“…Overviews of low-density gel-based biochip or hydrogel biochip technology and applications in different fields exemplifying diagnostics from infectious diseases to protein oncological markers have been published recently (Mikhailovich et al, 2008;Rubina et al, 2008). Principal difference of gel-based biochip technology comparing with other matrix microarrays is an immobilization of identifying probes in semi-spherical three-dimensional (3-D) gel elements instead of the flat supporting surface.…”

Microfluidic production of single micrometer-sized hydrogel beads utilizing droplet dissolution in a polar solvent

“…Hydrogels are also employed as three-dimensional scaffolds for constructing living tissue models and as matrices for biomolecule separation and analysis. [1][2][3] Spherical beads are one of the most common forms of hydrogels, largely because of the ease of its preparation and manipulation. In general, the physicochemical characteristics and applications of hydrogel beads are closely associated with their size and monodispersity.…”